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phylosignal

Install

To install the package you can use remotes:

remotes::install_github("fkeck/phylosignal")

Getting started

A quick overview of the package link

Plotting phylogenies and traits values link

Article

Keck F., Rimet F., Bouchez A. & Franc A. (2016) phylosignal: an R package to measure, test, and explore the phylogenetic signal. Ecology and Evolution 6 (9), 2774–2780. http://onlinelibrary.wiley.com/doi/10.1002/ece3.2051/epdf

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Version

Install

install.packages('phylosignal')

Monthly Downloads

478

Version

1.3.1

License

GPL-3

Maintainer

Francois Keck

Last Published

October 12th, 2023

Functions in phylosignal (1.3.1)

Computes permutation test for Blomberg's K Star

phyloCorrelogram

Phylogenetic correlogram

Computes phylogenetic signal for bootstrapped replicates of a phylogeny.

Phylogenetic signal estimation as a fraction of a Brownian Motion process.

Computes log-likelihood for data and a given value of Pagel's Lambda

Reordering vector or matrix of settings.

multiplot.phylo4d

Plots of Traits Values along a Phylogeny

Computes phylogenetic signal at each internal node of a phylogeny

Simulate the behaviour of phylogenetic signal statistics with a given phylogeny

Phylogeny and pollution sensitivity of diatoms

print.phylosimsignal

Print signal estimation as a fraction of a Brownian Motion process.

plot.graphclust

Plot phylogenetically constrained clustering

Read a phylo4d object from files

rTraitContWeight

Traits Values Simulation

print.graphclust

#' Print results of phylogenetically constrained clustering

plot.phylocorrelogram

Plot a phylogenetic correlogram

Plot phylosim object

plot.phylosimsignal

Plot signal estimation as a fraction of a Brownian Motion process.

Phylogenetic weights matrix

subsetPhyloSimSignal

phyloSimSignal subsetting

Computes phylogenetic signal with different methods

Pairwise Distance from Regularly Distributed Points

dotplot.phylo4d

Dotplot of Traits Values along a Phylogeny

ID of direct descents

Phylogenetically constrained clustering

Names of descents

Palette of evenly distributed colors

barplot.phylo4d

Barplot of Traits Values along a Phylogeny

Focus on sub parts of a plot

matchTipsAndTraits

Match matrix row/col names with phylo4d tips/traits

gridplot.phylo4d

Gridplot of Traits Values along a Phylogeny

Local Indicator of Phylogenetic Association

.layouterizeRatio

Set layout for plots

Computes permutation test for Moran's I

Test Pagel's Lambda Optimize Pagel's Lambda and do a likelihood ratio test.

Computes permutation test for Blomberg's K

Set layout for plots

Mantel statistic